/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.variant;
import org.apache.log4j.Logger;
import org.broad.igv.track.AttributeManager;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackMenuUtils;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.action.GroupTracksMenuAction;
import org.broad.igv.ui.panel.IGVPopupMenu;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.*;
import java.util.List;
/**
* User: Jesse Whitworth
* Date: Jul 16, 2010
*/
public class VariantMenu extends IGVPopupMenu {
private static Logger log = Logger.getLogger(VariantMenu.class);
private VariantTrack track;
private Collection<String> selectedSamples;
static boolean depthSortingDirection;
static boolean genotypeSortingDirection;
static boolean sampleSortingDirection;
static boolean qualitySortingDirection;
static boolean hasReviewTrack = false;
public VariantMenu(final VariantTrack variantTrack, final Variant variant) {
super();
this.track = variantTrack;
if (track.hasAlignmentFiles()) {
selectedSamples = track.getSelectedSamples();
}
//Title
JLabel popupTitle = new JLabel("<html><b>" + this.track.getName(), JLabel.LEFT);
Font newFont = getFont().deriveFont(Font.BOLD, 12);
popupTitle.setFont(newFont);
add(popupTitle);
//Change Track Settings
addSeparator();
List<Track> selectedTracks = Arrays.asList((Track) variantTrack);
add(TrackMenuUtils.getTrackRenameItem(selectedTracks));
add(TrackMenuUtils.getChangeFontSizeItem(selectedTracks));
addSeparator();
JLabel colorSiteByItem = new JLabel("<html> <b>Color By", JLabel.LEFT);
add(colorSiteByItem);
add(getColorBandByAllelFrequency());
add(getColorBandByAlleleFraction());
//Hides
if (track.isEnableMethylationRateSupport()) {
addSeparator();
JLabel colorByItem = new JLabel("<html> <b>Color Samples By", JLabel.LEFT);
add(colorByItem);
add(getColorByGenotype());
add(getColorByMethylationRate());
}
//add(getRenderIDItem());
//Sorter
addSeparator();
for (JMenuItem item : getSortMenuItems(variant)) {
add(item);
item.setEnabled(variant != null);
}
if (AttributeManager.getInstance().getVisibleAttributes().size() > 0) {
addSeparator();
add(getGenotypeGroupItem());
}
//Variant Information
addSeparator();
JLabel displayHeading = new JLabel("Display Mode", JLabel.LEFT);
add(displayHeading);
for (JMenuItem item : getDisplayModeItems()) {
add(item);
}
addSeparator();
JMenuItem item = new JMenuItem("Change Squished Row Height...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
int currentValue = track.getSquishedHeight();
Integer newValue = TrackMenuUtils.getIntegerInput("Squished row height", currentValue);
if (newValue != null) {
track.setSquishedHeight(newValue);
IGV.getInstance().getContentPane().repaint();
}
}
});
add(item);
add(getHideFilteredItem());
add(getFeatureVisibilityItem());
if (track.hasAlignmentFiles()) {
addSeparator();
add(getLoadBamsItem());
}
}
private JMenuItem getFeatureVisibilityItem() {
JMenuItem item = new JMenuItem("Set Feature Visibility Window...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
changeVisibilityWindow();
IGV.getInstance().getContentPane().repaint();
}
});
return item;
}
private JMenuItem getColorBandByAllelFrequency() {
final JMenuItem item = new JCheckBoxMenuItem("Allele Frequency", track.getSiteColorMode() == VariantTrack.ColorMode.ALLELE_FREQUENCY);
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setSiteColorMode(VariantTrack.ColorMode.ALLELE_FREQUENCY);
IGV.getInstance().getContentPane().repaint();
}
});
return item;
}
private JMenuItem getColorBandByAlleleFraction() {
final JMenuItem item = new JCheckBoxMenuItem("Allele Fraction", track.getSiteColorMode() == VariantTrack.ColorMode.ALLELE_FRACTION);
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setSiteColorMode(VariantTrack.ColorMode.ALLELE_FRACTION);
IGV.getInstance().getContentPane().repaint();
}
});
return item;
}
private JMenuItem getColorByGenotype() {
final JMenuItem item = new JCheckBoxMenuItem("Genotype", track.getColorMode() == VariantTrack.ColorMode.GENOTYPE);
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setColorMode(VariantTrack.ColorMode.GENOTYPE);
IGV.getInstance().getContentPane().repaint();
}
});
return item;
}
private JMenuItem getColorByMethylationRate() {
final JMenuItem item = new JCheckBoxMenuItem("Methylation Rate", track.getColorMode() == VariantTrack.ColorMode.METHYLATION_RATE);
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setColorMode(VariantTrack.ColorMode.METHYLATION_RATE);
IGV.getInstance().getContentPane().repaint();
}
});
return item;
}
private JMenuItem getHideFilteredItem() {
JMenuItem item = new JCheckBoxMenuItem("Suppress Filtered Sites", track.getHideFiltered());
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setHideFiltered(!track.getHideFiltered());
IGV.getInstance().getContentPane().repaint();
}
});
return item;
}
public JMenuItem getGenotypeSortItem(final Variant variant) {
JMenuItem item = new JMenuItem("Sort By Genotype");
if (variant != null) {
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
GenotypeComparator compare = new GenotypeComparator(variant);
genotypeSortingDirection = !genotypeSortingDirection;
track.sortSamples(compare);
IGV.getInstance().getContentPane().repaint();
}
});
}
return item;
}
public JMenuItem getGenotypeGroupItem() {
JMenuItem item = new JMenuItem("Group By...");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
(new GroupTracksMenuAction("", 0, IGV.getInstance())).doGroupBy();
}
});
item.setEnabled(AttributeManager.getInstance().getVisibleAttributes().size() > 0);
return item;
}
public JMenuItem getSampleNameSortItem(final Variant variant) {
JMenuItem item = new JMenuItem("Sort By Sample Name");
if (variant != null) {
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
Comparator<String> compare = new Comparator<String>() {
public int compare(String o, String o1) {
if (sampleSortingDirection) {
return o.compareTo(o1);
} else {
return o1.compareTo(o);
}
}
};
sampleSortingDirection = !sampleSortingDirection;
track.sortSamples(compare);
IGV.getInstance().getContentPane().repaint();
}
});
}
return item;
}
public JMenuItem getDepthSortItem(final Variant variant) {
JMenuItem item = new JMenuItem("Sort By Depth");
if (variant != null) {
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
DepthComparator compare = new DepthComparator(variant);
depthSortingDirection = !depthSortingDirection;
track.sortSamples(compare);
IGV.getInstance().getContentPane().repaint();
}
});
}
return item;
}
public JMenuItem getQualitySortItem(final Variant variant) {
JMenuItem item = new JMenuItem("Sort By Quality");
if (variant != null) {
double quality = variant.getPhredScaledQual();
if (quality > -1) {
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
QualityComparator compare = new QualityComparator(variant);
qualitySortingDirection = !qualitySortingDirection;
track.sortSamples(compare);
IGV.getInstance().getContentPane().repaint();
}
});
} else {
item.setEnabled(false);
}
}
return item;
}
public void changeVisibilityWindow() {
TrackMenuUtils.changeFeatureVisibilityWindow(Arrays.asList((Track) track));
}
public Collection<JMenuItem> getSortMenuItems(Variant variant) {
java.util.List<JMenuItem> items = new ArrayList<JMenuItem>();
items.add(getGenotypeSortItem(variant));
items.add(getSampleNameSortItem(variant));
items.add(getDepthSortItem(variant));
items.add(getQualitySortItem(variant));
return items;
}
public List<JMenuItem> getDisplayModeItems() {
List<JMenuItem> items = new ArrayList();
ButtonGroup group = new ButtonGroup();
Track.DisplayMode displayMode = track.getDisplayMode();
JRadioButtonMenuItem m1 = new JRadioButtonMenuItem("Collapsed");
m1.setSelected(displayMode == Track.DisplayMode.COLLAPSED);
m1.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setDisplayMode(Track.DisplayMode.COLLAPSED);
IGV.getInstance().doRefresh();
}
});
JRadioButtonMenuItem m2 = new JRadioButtonMenuItem("Squished");
m2.setSelected(displayMode == Track.DisplayMode.SQUISHED);
m2.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setDisplayMode(Track.DisplayMode.SQUISHED);
IGV.getInstance().doRefresh();
}
});
JRadioButtonMenuItem m3 = new JRadioButtonMenuItem("Expanded");
m3.setSelected(displayMode == Track.DisplayMode.EXPANDED);
m3.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.setDisplayMode(Track.DisplayMode.EXPANDED);
IGV.getInstance().doRefresh();
}
});
items.add(m1);
items.add(m2);
items.add(m3);
group.add(m1);
group.add(m2);
group.add(m3);
return items;
}
/**
* Load bam files associated with the selected samples (experimental).
*
* @return
*/
private JMenuItem getLoadBamsItem() {
final JMenuItem item = new JMenuItem("Load alignments");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent evt) {
track.loadSelectedBams();
}
});
item.setEnabled(selectedSamples != null && selectedSamples.size() > 0);
return item;
}
static class GenotypeComparator implements Comparator<String> {
Variant variant;
GenotypeComparator(Variant variant) {
this.variant = variant;
}
public int compare(String e1, String e2) {
int genotype1 = classifyGenotype(variant.getGenotype(e1));
int genotype2 = classifyGenotype(variant.getGenotype(e2));
if (genotype2 == genotype1) {
return 0;
} else if (genotype2 > genotype1) {
return genotypeSortingDirection ? 1 : -1;
} else {
return genotypeSortingDirection ? -1 : 1;
}
}
private int classifyGenotype(Genotype genotype) {
if (genotype.isNoCall()) {
return genotypeSortingDirection ? 1 : 10;
} else if (genotype.isHomVar()) {
return 4;
} else if (genotype.isHet()) {
return 3;
} else if (genotype.isHomRef()) {
return genotypeSortingDirection ? 2 : 9;
}
return -1; //Unknown
}
}
static class DepthComparator implements Comparator<String> {
Variant variant;
DepthComparator(Variant variant) {
this.variant = variant;
}
public int compare(String s1, String s2) {
double readDepth1 = variant.getGenotype(s1).getAttributeAsDouble("DP");
double readDepth2 = variant.getGenotype(s2).getAttributeAsDouble("DP");
int sign = depthSortingDirection ? -1 : 1;
return sign * Double.compare(readDepth1, readDepth2);
}
}
static class QualityComparator implements Comparator<String> {
Variant variant;
QualityComparator(Variant variant) {
this.variant = variant;
}
public int compare(String s1, String s2) {
double qual1 = variant.getGenotype(s1).getPhredScaledQual();
double qual2 = variant.getGenotype(s2).getPhredScaledQual();
int sign = qualitySortingDirection ? -1 : 1;
return sign * Double.compare(qual1, qual2);
}
}
}